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tcr_sri003 [2020/12/17 09:39] – tmatejuktcr_sri003 [2023/08/01 01:08] (current) – external edit 127.0.0.1
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 ==== example file ==== ==== example file ====
 +Create new folder for example file :
 +   mkdir ~/lammps_29Oct20_example
 +
 It is recommended that you test this script before you try to run your own LAMMPS problems. It is recommended that you test this script before you try to run your own LAMMPS problems.
  
 The example is a Lennard-Jones melt in a 3D box. The Lennard-Jones force has a cutoff at r = 2.5 sigma, where sigma is the distance at which the interparticle potential is zero. The system includes 32,000 atoms, and is to be modeled for 1000 time steps. The example is a Lennard-Jones melt in a 3D box. The Lennard-Jones force has a cutoff at r = 2.5 sigma, where sigma is the distance at which the interparticle potential is zero. The system includes 32,000 atoms, and is to be modeled for 1000 time steps.
  
-Create new folder for example file : +Store below in the filename ''in.lj'', under ''~/lammps_29Oct20_example/'':
-   mkdir ~/lammps_29Oct20_example +
- +
-The example is stored in the file in.lj, and reads as follows:+
 <code> <code>
 # 3d Lennard-Jones melt # 3d Lennard-Jones melt
Line 50: Line 50:
 variable y index 1 variable y index 1
 variable z index 1 variable z index 1
-variable t index 20000+variable t index 200000
  
 variable xx equal 20*$x variable xx equal 20*$x
Line 74: Line 74:
  
 fix      1 all nve fix      1 all nve
-thermo   1000+thermo   100
 run      $t run      $t
 </code> </code>
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 Use LAMMPS 29Oct20. This description assumes that path to binaries is ''/home/users/${USER}/soft/lammps_29Oct20/bin'' and example file ''in.lj'' is under ''/home/users/${USER}/lammps_29Oct20_example''. Use bellow ''lammps_29Oct20-test.sbatch'' file to run computation. Use LAMMPS 29Oct20. This description assumes that path to binaries is ''/home/users/${USER}/soft/lammps_29Oct20/bin'' and example file ''in.lj'' is under ''/home/users/${USER}/lammps_29Oct20_example''. Use bellow ''lammps_29Oct20-test.sbatch'' file to run computation.
   #!/bin/bash -l   #!/bin/bash -l
-  #SBATCH --job-name="lammps example N2_n32"+  #SBATCH --job-name="lammps-example-N2_n32"
   #SBATCH --nodes=2                   # number of computing_nodes   #SBATCH --nodes=2                   # number of computing_nodes
   #SBATCH --ntasks=32                 # number of CPU's ( 16*computing_nodes )   #SBATCH --ntasks=32                 # number of CPU's ( 16*computing_nodes )
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   T2=`date +%s`   T2=`date +%s`
   echo -e "stop ${T2}\t start ${T1}\t ${SLURM_NNODES}"   echo -e "stop ${T2}\t start ${T1}\t ${SLURM_NNODES}"
- 
- 
-FIXME 
- 
-FIXME 
- 
-FIXME 
- 
-FIXME 
- 
-FIXME 
  
 ==== performance tests ==== ==== performance tests ====
-Bellow results show time of computation in function of used resources (computation scalability) for a specific computational task done with ''pw.x'' program.+Bellow results show time of computation in function of used resources (computation scalability) for a specific computational task ''lammps_29Oct20-test.sbatch''.
  
 Assigning a larger amount of computing nodes does not always lead to a (efficient) reduction in computing time (wall-time of the job). To find the most appropriate number of nodes for a specific type of job, it is essential to run one's own benchmarks. In general, parallel <color #22b14c>jobs should scale to at least 70% efficiency for the sake of other TCR users</color>. One user using twice the resources to squeeze out 10% more performance may be keeping other users from working at all. Assigning a larger amount of computing nodes does not always lead to a (efficient) reduction in computing time (wall-time of the job). To find the most appropriate number of nodes for a specific type of job, it is essential to run one's own benchmarks. In general, parallel <color #22b14c>jobs should scale to at least 70% efficiency for the sake of other TCR users</color>. One user using twice the resources to squeeze out 10% more performance may be keeping other users from working at all.
  
-Bellow results should be consider as results of this specific computational task on this specific hardware (TCR cluster) and not overall benchmark for Quantum Espresso software suite.+Bellow results should be consider as results of this specific computational task on this specific hardware (TCR cluster) and not overall benchmark for LAMMPS software.
  
-{{ tcr:qe65_tcr_result_001.png?nolink|}} 
 ^nodes ^min [s] ^avg [s] ^median [s] ^max [s] ^efficiency [%] ^ ^nodes ^min [s] ^avg [s] ^median [s] ^max [s] ^efficiency [%] ^
-|1 |1862 |2065.75 |2126 |2149 |<color #22b14c>100.00%</color>| +|1 |349 |351.67 |349 |357 |<color #22b14c>100.00%</color>| 
-|2 |1105 |1192.75 |1157.5 |1351 |<color #22b14c>84.25%</color>| +|2 |206 |209.33 |207 |215 |<color #22b14c>84.71%</color>| 
-|3 |763 |770 |768.5 |780 |<color #22b14c>81.35%</color>| +|3 |156 |156.33 |156 |157 |<color #22b14c>74.57%</color>| 
-|4 |798 |1026.25 |868.5 |1570 |58.33%| +|4 |128 |128.67 |129 |129 |68.16%| 
-|5 |571 |589.75 |574 |640 |65.22%| +|5 |121 |121.33 |121 |122 |57.69%| 
-|6 |488 |536 |525.5 |605 |63.59%| +|6 |111 |111 |111 |111 |52.40%| 
-|7 |372 |502.25 |414.5 |808 |<color #22b14c>71.51%</color>| +|7 |92 |93 |93 |94 |54.19%| 
-|8 |375 |489.75 |408.5 |767 |62.07%| +|8 |88 |88.67 |89 |89 |49.57%| 
-|9 |324 |403.75 |346.5 |598 |63.85%| +|9 |83 |84 |84 |85 |46.72%|
-|10 |327 |456.25 |465.5 |567 |56.94%| +
-|12 |285 |429.4 |375 |609 |54.44%| +
-|16 |228 |274.25 |281.5 |306 |51.04%| +
- +
- +
  
 *) values (min, avg, median, max, efficiency) do not include failed runs \\ *) values (min, avg, median, max, efficiency) do not include failed runs \\
 +*) results are from 3 runs \\
 *) efficiency as ''t1 / ( nodes * tn )'' ( where t1 is min computation time at one node, tn is min computation time on N nodes ) \\ *) efficiency as ''t1 / ( nodes * tn )'' ( where t1 is min computation time at one node, tn is min computation time on N nodes ) \\
  
-example source) https://arc.vt.edu/userguide/lammps/+==== other ==== 
 +above desciption uses default settings and do not include any extra LAMMPS packages that you may require. More about LAMMPS' package at  [[https://lammps.sandia.gov/doc/Build_package.html]] . 
 + 
 +*) [[https://arc.vt.edu/userguide/lammps/]]
tcr_sri003.1608194360.txt.gz · Last modified: 2023/08/01 06:38 (external edit)

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